1t8s

;Crystal Structure of E.coli AMP Nucleosidase complexed with formicin 5'-monophosphate ;

Method: X-RAY DIFFRACTION D_max: 125.7 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1t8s
沉积日期 deposition_date	2004-05-13
结构标题 title	;Crystal Structure of E.coli AMP Nucleosidase complexed with formicin 5'-monophosphate ;
关键词 keywords	ALPHA-BETA-ALPHA SANDWICH, ALPHA-BETA FOLD, HYDROLASE; HYDROLASE
实验方法 method	X-RAY DIFFRACTION

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2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	42.25 Å
回转半径 Rg (电子) rg_electron	41.43 Å
零角强度 I(0) i0	1337960000.00
分子量 molecular_weight	300860.0 kDa
排除体积 excluded_volume	375020 Å³
包络体积 envelope_volume	492080 Å³
水化壳体积 shell_volume	91181 Å³
包络直径 envelope_diameter	129.9 Å
壳层 Rg shell_rg	52.65 Å
包络 Rg envelope_rg	40.81 Å
形状 Rg shape_rg	41.44 Å
总 Rg total_rg	41.86 Å
总原子数 total_atoms	21177
残基数 n_residues	2635
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	125.7 Å
Rg (实空间) rg_real	41.93 Å
Rg 误差 (实空间) rg_real_error	0.67 Å
I(0) (实空间) i0_real	1.3380e+09
I(0) 误差 (实空间) i0_real_error	2.0000e+07
Rg (倒空间) rg_reciprocal	42.25 Å
I(0) (倒空间) i0_reciprocal	1338000000.0000
解质量估计 total_estimate	0.8986
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	57.8 Å
偏度 Skewness skewness	-0.012
峰度 Kurtosis kurtosis	-0.578
角度范围 angular_range	— – 0.1850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	241900000.0000
实空间数据点数 n_real_points	38
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.931; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.953; Smooth: 0.930

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4. 晶体学与实验 4. Crystallography & Experiment

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5. 实体与聚合体信息 (3)

Entity 1 polymer

描述 description	AMP nucleosidase
分子量 formula_weight	54244.3 kDa
EC 编号 ec_number	3.2.2.4
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F
原子数 atom_count	21455

MNNKGSGLTPAQALDKLDALYEQSVVALRNAIGNYITSGELPDENARKQGLFVYPSLTVTWDGSTTNPPKTRAFGRFTHAGSYTTTITRPTLFRSYLNEQLTLLYQDYGAHISVQPSQHEIPYPYVIDGSELTLDRSMSAGLTRYFPTTELAQIGDETADGIYHPTEFSPLSHFDARRVDFSLARLRHYTGTPVEHFQPFVLFTNYTRYVDEFVRWGCSQILDPDSPYIALSCAGGNWITAETEAPEEAISDLAWKKHQMPAWHLITADGQGITLVNIGVGPSNAKTICDHLAVLRPDVWLMIGHCGGLRESQAIGDYVLAHAYLRDDHVLDAVLPPDIPIPSIAEVQRALYDATKLVSGRPGEEVKQRLRTGTVVTTDDRNWELRYSASALRFNLSRAVAIDMESATIAAQGYRFRVPYGTLLCVSDKPLHGEIKLPGQANRFYEGAISEHLQIGIRAIDLLRAEGDRLHSRKLRTFNEPPFR

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	FORMYCIN-5'-MONOPHOSPHATE
分子量 formula_weight	347.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 3 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	278

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6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1t8sa_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.56 — Phosphorylase/hydrolase-like
超家族 Superfamily superfamily	c.56.2 — Purine and uridine phosphorylases
家族 Family family	c.56.2.1 — Purine and uridine phosphorylases

结构域编号 domain_id	d1t8sb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.56 — Phosphorylase/hydrolase-like
超家族 Superfamily superfamily	c.56.2 — Purine and uridine phosphorylases
家族 Family family	c.56.2.1 — Purine and uridine phosphorylases

结构域编号 domain_id	d1t8sc_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.56 — Phosphorylase/hydrolase-like
超家族 Superfamily superfamily	c.56.2 — Purine and uridine phosphorylases
家族 Family family	c.56.2.1 — Purine and uridine phosphorylases

结构域编号 domain_id	d1t8sd_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.56 — Phosphorylase/hydrolase-like
超家族 Superfamily superfamily	c.56.2 — Purine and uridine phosphorylases
家族 Family family	c.56.2.1 — Purine and uridine phosphorylases

结构域编号 domain_id	d1t8se_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.56 — Phosphorylase/hydrolase-like
超家族 Superfamily superfamily	c.56.2 — Purine and uridine phosphorylases
家族 Family family	c.56.2.1 — Purine and uridine phosphorylases

结构域编号 domain_id	d1t8sf_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.56 — Phosphorylase/hydrolase-like
超家族 Superfamily superfamily	c.56.2 — Purine and uridine phosphorylases
家族 Family family	c.56.2.1 — Purine and uridine phosphorylases

CATH v4.4 (12 domains)

结构域编号 domain_id	1t8sA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1730 — amp nucleosidase, domain 1
同源超家族 H-superfamily homologous superfamily	10 — AMP nucleoside phosphorylase, N-terminal domain

结构域编号 domain_id	1t8sA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1580 — Nucleoside phosphorylase domain

结构域编号 domain_id	1t8sB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1730 — amp nucleosidase, domain 1
同源超家族 H-superfamily homologous superfamily	10 — AMP nucleoside phosphorylase, N-terminal domain

结构域编号 domain_id	1t8sB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1580 — Nucleoside phosphorylase domain

结构域编号 domain_id	1t8sC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1730 — amp nucleosidase, domain 1
同源超家族 H-superfamily homologous superfamily	10 — AMP nucleoside phosphorylase, N-terminal domain

结构域编号 domain_id	1t8sC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1580 — Nucleoside phosphorylase domain

结构域编号 domain_id	1t8sD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1730 — amp nucleosidase, domain 1
同源超家族 H-superfamily homologous superfamily	10 — AMP nucleoside phosphorylase, N-terminal domain

结构域编号 domain_id	1t8sD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1580 — Nucleoside phosphorylase domain

结构域编号 domain_id	1t8sE01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1730 — amp nucleosidase, domain 1
同源超家族 H-superfamily homologous superfamily	10 — AMP nucleoside phosphorylase, N-terminal domain

结构域编号 domain_id	1t8sE02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1580 — Nucleoside phosphorylase domain

结构域编号 domain_id	1t8sF01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1730 — amp nucleosidase, domain 1
同源超家族 H-superfamily homologous superfamily	10 — AMP nucleoside phosphorylase, N-terminal domain

结构域编号 domain_id	1t8sF02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1580 — Nucleoside phosphorylase domain

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7. 引用文献 (1)

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晶胞边长 a length_a	246.240 Å
晶胞边长 b length_b	246.240 Å
晶胞边长 c length_c	111.130 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	48

空间群 space_group	P 42 21 2
空间群编号 int_tables_number	94
晶系 crystal_system	—

分辨率 resolution	2.600 Å
最低分辨率 resolution_low	36.750 Å
R 因子 r_factor	0.2260
R_work r_work	0.2260
R_free r_free	0.2560

fit	/app/data/saxs_computation/t8/1t8s/1t8s.fit
pddf	/app/data/pr_computation/t8/1t8s/1t8s.pr.out
profile	/app/data/saxs_computation/t8/1t8s/1t8s.dat